I've always had a soft spot for "Swordbreaker" from "Lost Universe" (an anime that never really became very successful, done by the same people who did "The Slayers" and "Trigun").
While my opinions on the show itself were mixed, I think the Lexx from the TV show "Lexx" was pretty awesome too, it's pretty much a giant bug flying through space that can blow up planets with it's eyes. It's piloted by dysfunctional twits though. "Lexx" is pretty much Farscape's "Moya" enlarged to gigantic size and loaded with planetbusting firepower. Albeit "Moya" got to be in a much better show overall (in my opinion).
It's also not a ship per se, but I've also felt Larry Niven's "Ring World" was one of the more conceptually awesome ideas out there. Sure Dyson spheres are bigger as an concept, but the Ring World was just kind of cool.